RELION Multibody Refinement

For general information on job submission, please see here.

The following are details related to RELION multibody refinement. For more information multibody refinement, please see this protocol.

Input particle stack format:

RELION-extracted particle stack. Click here to learn what this means.

This stack needs to be the same as that used during the RELION 3D refinement that was used to obtain the consensus 3D reconstruction.

Additional input files: Uploaded through ‘Browser Upload’

For multibody refinement, you will need all files associated with the consensus 3D refinement that is performed ahead of multibody refinement. This includes:

  • _optimiser.star
  • _sampling.star
  • _half1_model.star
  • _half1_class001.mrc
  • _half2_model.star
  • _half2_class001.mrc
  • _data.star

You will also need the associated masks and references. All files need to be included in single zipped file (.zip extension), which will be made from a directory that contains all masks and reference volumes. IMPORTANT:

  1. The unzipped directory name but the same as the zipped directory name (Mask-and-Ref/ is zipped into Mask-and-Ref.zip)
  2. All files must be in the directory
  3. There must be a STAR file named multibody-masks.star in the zipped directory.
  4. The multibody-masks.star file must have correct paths to each file in this directory.
  • To see an example .zip file, you can download an example here.
  • Upload this .zip file via file browser.
  • To zip a directory:
    • $ zip -r Mask-and-Ref.zip Mask-and-Ref/
  • Contents of Mask-and-Ref/multibody-masks.star:

data_
loop_
_rlnBodyMaskName
_rlnBodyRotateRelativeTo
_rlnBodySigmaAngles
_rlnBodySigmaOffset
_rlnBodyReferenceName
Mask-and-Ref/CORE_mask.mrc 2 10 2 Mask-and-Ref/CORE_ref.mrc
Mask-and-Ref/FOOT_mask.mrc 1 10 2 Mask-and-Ref/FOOT_ref.mrc
Mask-and-Ref/HELICASE_mask.mrc 1 15 3 Mask-and-Ref/HELICASE_ref.mrc
Mask-and-Ref/SF3b_mask.mrc 1 20 5 Mask-and-Ref/SF3b_ref.mrc

 

Contents of Mask-and-Ref:

$ ls Mask-and-Ref/
CORE_mask.mrc  FOOT_mask.mrc  global_mask.mrc    HELICASE_ref.mrc      SF3b_mask.mrc
CORE_ref.mrc   FOOT_ref.mrc   HELICASE_mask.mrc  multibody-masks.star  SF3b_ref.mrc

Example listing of data uploads

NOTE: All RELION files are listed without any parent directories. E.g. run_it019_data.star is not Refine3D/job001/run_it019_data.star, with the exception of the uploaded particle stack (Extract/job001/particles.star)

Required input parameters:  

  1. Initial angular sampling, in degrees
  2. Initial offset range, in pixels
  3. Initial offset step, in pixels

Software citations:

“RELION: Implementation of a Bayesian approach to cryo-EM structure determination.” S.H.W. Scheres J. Struct. Biol. (2012) 180:519-530. Link

“Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION.” eLife. 2018 Jun 1;7:e36861. Link.